Antigen persists in discrete cell populations within the lymph node
Identification of an antigen archiving gene signature
Predicting antigen archiving ability
Antigen archiving is enhanced by sequential vaccinations
Antigen exchange with DCs correlates with levels of antigen archiving
Antigen archiving is impaired during CHIKV infection
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## time zone: America/Denver
## tzcode source: system (glibc)
##
## attached base packages:
## [1] grid tools stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] SpatialOmicsOverlay_1.0.0 umap_0.2.10.0
## [3] GeoMxWorkflows_1.6.0 GeomxTools_3.4.0
## [5] NanoStringNCTools_1.8.0 cli_3.6.1
## [7] devtools_2.4.5 usethis_2.2.2
## [9] here_1.0.1 broom_1.0.5
## [11] knitr_1.44 lubridate_1.9.3
## [13] forcats_1.0.0 stringr_1.5.0
## [15] dplyr_1.1.3 purrr_1.0.2
## [17] readr_2.1.4 tidyr_1.3.0
## [19] tibble_3.2.1 tidyverse_2.0.0
## [21] png_0.1-8 ComplexHeatmap_2.16.0
## [23] xlsx_0.6.5 openxlsx_4.2.5.2
## [25] qs_0.25.5 ggtree_3.8.2
## [27] MetBrewer_0.2.0 ggtrace_0.2.0.9000
## [29] ggtext_0.1.2 patchwork_1.1.3
## [31] colorblindr_0.1.0 colorspace_2.1-0
## [33] RColorBrewer_1.1-3 ggrepel_0.9.3
## [35] cowplot_1.1.1 ggbeeswarm_0.7.2
## [37] ggforce_0.4.1 scales_1.2.1
## [39] caret_6.0-94 lattice_0.21-8
## [41] ggplot2_3.4.4 furrr_0.3.1
## [43] future_1.33.0 ranger_0.15.1
## [45] rsample_1.2.0 gtools_3.9.4
## [47] boot_1.3-28.1 mixtools_2.0.0
## [49] GOSemSim_2.26.1 org.Mm.eg.db_3.17.0
## [51] AnnotationDbi_1.62.2 IRanges_2.34.1
## [53] S4Vectors_0.38.2 Biobase_2.60.0
## [55] BiocGenerics_0.46.0 msigdbr_7.5.1
## [57] enrichplot_1.20.3 clusterProfiler_4.8.3
## [59] biomaRt_2.56.1 gprofiler2_0.2.2
## [61] M3Drop_1.26.0 numDeriv_2016.8-1.1
## [63] djvdj_0.1.0 harmony_1.1.0
## [65] presto_1.0.0 data.table_1.14.8
## [67] Rcpp_1.0.11 clustifyrdata_1.1.0
## [69] clustifyr_1.12.0 SeuratObject_4.1.4
## [71] Seurat_4.4.0
##
## loaded via a namespace (and not attached):
## [1] igraph_1.5.1 ica_1.0-3
## [3] plotly_4.10.2 Formula_1.2-5
## [5] zlibbioc_1.46.0 tidyselect_1.2.0
## [7] bit_4.0.5 doParallel_1.0.17
## [9] clue_0.3-65 rjson_0.2.21
## [11] blob_1.2.4 urlchecker_1.0.1
## [13] S4Arrays_1.0.6 parallel_4.3.1
## [15] plotrix_3.8-4 ggplotify_0.1.2
## [17] outliers_0.15 askpass_1.2.0
## [19] openssl_2.1.1 goftest_1.2-3
## [21] kernlab_0.9-32 densEstBayes_1.0-2.2
## [23] uwot_0.1.16 shadowtext_0.1.2
## [25] curl_5.1.0 mime_0.12
## [27] evaluate_0.22 tidytree_0.4.5
## [29] tiff_0.1-12 leiden_0.4.3
## [31] stringi_1.7.12 pROC_1.18.5
## [33] backports_1.4.1 lmerTest_3.1-3
## [35] XML_3.99-0.14 httpuv_1.6.11
## [37] magrittr_2.0.3 rappdirs_0.3.3
## [39] splines_4.3.1 prodlim_2023.08.28
## [41] RApiSerialize_0.1.2 jpeg_0.1-10
## [43] ggraph_2.1.0 sctransform_0.4.0
## [45] sessioninfo_1.2.2 DBI_1.1.3
## [47] jquerylib_0.1.4 withr_2.5.1
## [49] systemfonts_1.0.4 class_7.3-22
## [51] rprojroot_2.0.3 lmtest_0.9-40
## [53] bdsmatrix_1.3-6 tidygraph_1.2.3
## [55] BiocManager_1.30.22 htmlwidgets_1.6.2
## [57] fs_1.6.3 SingleCellExperiment_1.22.0
## [59] segmented_1.6-4 labeling_0.4.3
## [61] cellranger_1.1.0 MatrixGenerics_1.12.3
## [63] reticulate_1.32.0 zoo_1.8-12
## [65] GGally_2.2.0 XVector_0.40.0
## [67] timechange_0.2.0 foreach_1.5.2
## [69] fansi_1.0.5 caTools_1.18.2
## [71] timeDate_4022.108 ggiraph_0.8.7
## [73] RSpectra_0.16-1 irlba_2.3.5.1
## [75] gridGraphics_0.5-1 ellipsis_0.3.2
## [77] lazyeval_0.2.2 yaml_2.3.7
## [79] survival_3.5-5 scattermore_1.2
## [81] crayon_1.5.2 RcppAnnoy_0.0.21
## [83] progressr_0.14.0 tweenr_2.0.2
## [85] later_1.3.1 ggridges_0.5.4
## [87] codetools_0.2-19 base64enc_0.1-3
## [89] GlobalOptions_0.1.2 profvis_0.3.8
## [91] KEGGREST_1.40.1 bbmle_1.0.25
## [93] Rtsne_0.16 shape_1.4.6
## [95] filelock_1.0.2 foreign_0.8-84
## [97] pkgconfig_2.0.3 xml2_1.3.5
## [99] EnvStats_2.8.1 GenomicRanges_1.52.1
## [101] aplot_0.2.2 spatstat.sparse_3.0-2
## [103] ape_5.7-1 viridisLite_0.4.2
## [105] xtable_1.8-4 plyr_1.8.9
## [107] httr_1.4.7 globals_0.16.2
## [109] hardhat_1.3.0 pkgbuild_1.4.2
## [111] beeswarm_0.4.0 htmlTable_2.4.2
## [113] checkmate_2.3.0 nlme_3.1-162
## [115] loo_2.6.0 HDO.db_0.99.1
## [117] dbplyr_2.3.4 lme4_1.1-35.1
## [119] digest_0.6.33 Matrix_1.6-1.1
## [121] farver_2.1.1 tzdb_0.4.0
## [123] reshape2_1.4.4 ModelMetrics_1.2.2.2
## [125] yulab.utils_0.1.0 viridis_0.6.4
## [127] rpart_4.1.19 glue_1.6.2
## [129] cachem_1.0.8 BiocFileCache_2.8.0
## [131] polyclip_1.10-6 Hmisc_5.1-1
## [133] generics_0.1.3 Biostrings_2.68.1
## [135] mvtnorm_1.2-3 parallelly_1.36.0
## [137] pkgload_1.3.3 statmod_1.5.0
## [139] minqa_1.2.6 pbapply_1.7-2
## [141] SummarizedExperiment_1.30.2 vroom_1.6.4
## [143] gson_0.1.0 utf8_1.2.3
## [145] gower_1.0.1 graphlayouts_1.0.2
## [147] StanHeaders_2.26.28 readxl_1.4.3
## [149] gridExtra_2.3 shiny_1.7.5
## [151] lava_1.7.3 GenomeInfoDbData_1.2.10
## [153] RCurl_1.98-1.12 memoise_2.0.1
## [155] rmarkdown_2.25 pheatmap_1.0.12
## [157] downloader_0.4 RANN_2.6.1
## [159] stringfish_0.15.8 spatstat.data_3.0-1
## [161] rstudioapi_0.15.0 cluster_2.1.4
## [163] QuickJSR_1.0.7 rstantools_2.3.1.1
## [165] spatstat.utils_3.0-3 hms_1.1.3
## [167] fitdistrplus_1.1-11 munsell_0.5.0
## [169] rlang_1.1.1 GenomeInfoDb_1.36.4
## [171] ipred_0.9-14 circlize_0.4.15
## [173] mgcv_1.8-42 xfun_0.40
## [175] remotes_2.4.2.1 recipes_1.0.8
## [177] iterators_1.0.14 matrixStats_1.0.0
## [179] reldist_1.7-2 abind_1.4-5
## [181] rstan_2.32.3 treeio_1.24.3
## [183] rJava_1.0-6 fftwtools_0.9-11
## [185] bitops_1.0-7 ps_1.7.5
## [187] promises_1.2.1 inline_0.3.19
## [189] scatterpie_0.2.1 RSQLite_2.3.1
## [191] qvalue_2.32.0 fgsea_1.26.0
## [193] DelayedArray_0.26.7 GO.db_3.17.0
## [195] compiler_4.3.1 RBioFormats_1.0.0
## [197] prettyunits_1.2.0 listenv_0.9.0
## [199] tensor_1.5 MASS_7.3-60
## [201] progress_1.2.2 uuid_1.1-1
## [203] BiocParallel_1.34.2 gridtext_0.1.5
## [205] EBImage_4.42.0 babelgene_22.9
## [207] spatstat.random_3.1-6 R6_2.5.1
## [209] fastmap_1.1.1 fastmatch_1.1-4
## [211] vipor_0.4.5 ROCR_1.0-11
## [213] ggstats_0.5.1 nnet_7.3-19
## [215] gtable_0.3.4 KernSmooth_2.23-21
## [217] miniUI_0.1.1.1 deldir_1.0-9
## [219] ggthemes_5.0.0 htmltools_0.5.6.1
## [221] RcppParallel_5.1.7 bit64_4.0.5
## [223] spatstat.explore_3.2-3 lifecycle_1.0.3
## [225] zip_2.3.0 processx_3.8.2
## [227] nloptr_2.0.3 callr_3.7.3
## [229] xlsxjars_0.6.1 sass_0.4.7
## [231] vctrs_0.6.3 spatstat.geom_3.2-5
## [233] DOSE_3.26.2 ggfun_0.1.3
## [235] sp_2.1-0 future.apply_1.11.0
## [237] entropy_1.3.1 bslib_0.5.1
## [239] pillar_1.9.0 magick_2.8.2
## [241] gplots_3.1.3 locfit_1.5-9.8
## [243] BiocStyle_2.28.1 jsonlite_1.8.7
## [245] GetoptLong_1.0.5